Simulation-based benchmarking of isoform quantification in single-cell RNA-seq

Abstract

Abstract Single-cell RNA-seq has the potential to facilitate isoform quantification as the confounding factor of a mixed population of cells is eliminated. However, best practice for using existing quantification methods has not been established. We carry out a benchmark for five popular isoform quantification tools. Performance is generally good for simulated data based on SMARTer and SMART-seq2 data. The reduction in performance compared with bulk RNA-seq is small. An important biological insight comes from our analysis of real data which shows that genes that express two isoforms in bulk RNA-seq predominantly express one or neither isoform in individual cells.

Keywords

• scRNA-seq
• Benchmark
• Isoform quantification
• Single cell
• Bulk RNA-seq